Getting Started: The Basics
Water, The chemistry of life.
Whenever we attempt to determine whether there is life as we know it on Mars
or other planets, scientists first seek to establish whether or not water is
present. Why? Because life on earth totally depends on water.
A High percentage of living things, both plant and animal are found in water.
All life on earth is thought to have arisen from water. The bodies of all living
organisms are composed largely of water. About 70 to 90 percent of all organic
matter is water.
The chemical reactions in all plants and animals that support life take place
in a water medium. Water not only provides the medium to make these life
sustaining reactions possible, but water itself is often an important reactant
or product of these reactions. In short, the chemistry of life is water
chemistry.
Water, the universal solvent
Water is a universal, superb solvent due to the marked
polarity of the water molecule and its tendency to form hydrogen bonds with
other molecules. One water molecule, expressed with the chemical symbol
H2O, consists of 2 hydrogen atoms and 1 oxygen atom.
Standing alone, the hydrogen atom contains one positive proton at its core with one negative electron revolving
around it in a three-dimensional shell. Oxygen, on the other hand, contains 8
protons in its nucleus with 8 electrons revolving around it. This is often shown
in chemical notation as the letter O surrounded by eight dots representing 4
sets of paired electrons.
The single hydrogen electron and the 8 electrons of oxygen are the key to the
chemistry of life because this is where hydrogen and oxygen atoms combine to
form a water molecule, or split to form ions.
Hydrogen tends to ionize by losing its single electron and form single H+
ions which are simply isolated protons since the hydrogen atom contains no
neutrons. A hydrogen bond occurs when the electron of a single hydrogen atom is
shared with another electronegative atom such as oxygen that lacks an
electron.
Polarity of water molecules
In a water molecule, two hydrogen atoms are covalently bonded to the oxygen
atom. But because the oxygen atom is larger than the hydrogens, its attraction
for the hydrogen's electrons is correspondingly greater so the electrons are
drawn closer into the shell of the larger oxygen atom and away from the hydrogen
shells. This means that although the water molecule as a whole is stable, the
greater mass of the oxygen nucleus tends to draw in all the electrons in the
molecule including the shared hydrogen electrons giving the oxygen portion of
the molecule a slight electronegative charge.
The shells of the hydrogen atoms, because their electrons are closer to the oxygen, take on a small
electropositive charge. This means water molecules have a tendency to form weak
bonds with water molecules because the oxygen end of the molecule is negative
and the hydrogen ends are positive.
A hydrogen atom, while remaining covalently bonded to the oxygen of its own
molecule, can form a weak bond with the oxygen of another molecule. Similarly,
the oxygen end of a molecule can form a weak attachment with the hydrogen ends
of other molecules. Because water molecules have this polarity, water is a
continuous chemical entity.
These weak bonds play a crucial role in stabilizing the shape of many of the
large molecules found in living matter. Because these bonds are weak, they are
readily broken and re-formed during normal physiological reactions. The
disassembly and re-arrangement of such weak bonds is in essence the chemistry of
life.
To illustrate water's ability to break down other substances, consider the simple example of putting a small amount of
table salt in a glass of tap water. With dry salt (NaCl) the attraction between
the electropositive sodium (Na+) and electronegative chlorine (Cl-) atoms of
salt is very strong until it is placed in water. After salt is placed in water,
the attraction of the electronegative oxygen of the water molecule for the
positively charged sodium ions, and the similar attraction of the
electropositive hydrogen ends of the water molecule for the negatively charged
chloride ions, are greater than the mutual attraction between the outnumbered
Na+ and Cl- ions. In water the ionic bonds of the sodium chloride molecule are
broken easily because of the competitive action of the numerous water molecules.
As we can see from this simple example, even the delicate configuration of
individual water molecules enables them to break relatively stronger bonds by
converging on them. This is why we call water the universal solvent. It is a
natural solution that breaks the bonds of larger, more complex molecules. This
is the chemistry of life on earth, in water and on land.
Oxidation-reduction reactions
Basically, reduction means the addition of an electron (e-), and its
converse, oxidation means the removal of an electron. The addition of an
electron, reduction, stores energy in the reduced compound. The removal of an
electron, oxidation, liberates energy from the oxidized compound. Whenever one
substance is reduced, another is oxidized.
To clarify these terms, consider any two molecules, A and B, for example.
When molecules A and B come into contact, here is what happens:
- B grabs an electron from molecule A.
- Molecule A has been oxidized because it has lost an electron.
-
The net charge of B has been reduced because it has gained a negative
electron (e-).
In biological systems, removal or addition of an electron constitutes the
most frequent mechanism of oxidation-reduction reactions. These
oxidation-reduction reactions are frequently called redox reactions.
Acids and Bases
An acid is a substance that increases the concentration of hydrogen ions (H+)
in water. A base is a substance that decreases the concentration of hydrogen
ions, in other words, increasing the concentration of hydroxide ions OH-.
The degree of acidity or alkalinity of a solution is measured in terms of a
value known as pH, which is the negative logarithm of the concentration of
hydrogen ions:
pH = 1/log[H+] = -log[H+]
What is pH?
On the pH scale, which ranges from 0 on the acidic end to 14 on the alkaline
end, a solution is neutral if its pH is 7. At pH 7, water contains equal
concentrations of H+ and OH- ions. Substances with a pH less than 7 are acidic
because they contain a higher concentration of H+ ions. Substances with a pH
higher than 7 are alkaline because they contain a higher concentration of OH-
than H+. The pH scale is a log scale so a change of one pH unit means a tenfold
change in the concentration of hydrogen ions.
Importance of balancing pH
Living things are extremely sensitive to pH and function best (with certain
exceptions, such as certain portions of the digestive tract) when solutions are
nearly neutral. Most interior living matter (excluding the cell nucleus) has a
pH of about 6.8.
Blood plasma and other fluids that surround the cells in the body have a pH of
7.2 to 7.3. Numerous special mechanisms aid in stabilizing these fluids so that
cells will not be subject to appreciable fluctuations in pH. Substances which
serve as mechanisms to stabilize pH are called buffers. Buffers have the
capacity to bond ions and remove them from solution whenever their concentration
begins to rise. Conversely, buffers can release ions whenever their
concentration begins to fall. Buffers thus help to minimize the fluctuations in
pH. This is an important function because many biochemical reactions normally
occurring in living organisms either release or use up ions.
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